Exon type problem asking...

[edge]

As I know, normally the output result of gene prediction program will shown that exon type consist of initial, internal, terminal and single.
Does anybody can share that how can we determine the initial, internal, terminal and single of gene structure?
How can we classify the exon type under initial, internal, terminal and single?
Thanks a lot for sharing.

[steven]

As I know, normally the output result of gene prediction program will shown that exon type consist of initial, internal, terminal and single.
Does anybody can share that how can we determine the initial, internal, terminal and single of gene structure?
How can we classify the exon type under initial, internal, terminal and single?
Thanks a lot for sharing.

Their boundaries differ (not the same type of biological signal):
- Initial exons start with a TSS (transcription start site) at the 5' end, and finishes with a donor splice site at the 3' end.
- Internal exons start with an acceptor splice site (5') and finishes by a donor (3').
- Terminal exons start with an acceptor and terminates on a polyadenylation site (cleavage point at the end of the mRNA).
- Single exons have no introns, and go directly from the TSS to the polyA.

Note that some gene finders only consider the coding parts of the exons (CDS) - for those, replace "TSS" by "translation start codon" (usually ATG) and "polyA" by "translation stop codon" (usually TAA/TAG/TGA).

The detection of these biological signals and the estimation of their "strength" is an important component of the -protein coding- gene finding process.

Hope it helps,
s.

[edge]

Hi Steven,

Really thanks a lot for your explanation in detail. I very appreciate it
Regarding the acceptor splice site and donor splice site that you mentioned, is it caused by the alternative splicing happened within the mRNA processing?
Besides that, do you have the experience in gff3 format and annotation program?
I got deal with some annotation tool recently. I feel a bit confusing about some of their output result analysis
From the output result of that annotation program, it seems like shown that "gene = mRNA" region and "exon = CDS" region?
If you got experience in exploring annotation program, can I ask you opinions about it too?
Thanks again and a lot for your help first

[steven]

Hi Steven,

Really thanks a lot for your explanation in detail. I very appreciate it
Regarding the acceptor splice site and donor splice site that you mentioned, is it caused by the alternative splicing happened within the mRNA processing?

Yes -not necessarily alternative though. Unless of course splice sites are the cause, and splicing the consequence.. like in the egg mystery
I would recommend some reading on basic molecular biology first: understanding gene prediction requires some knowledge on gene structure and expression.

Besides that, do you have the experience in gff3 format and annotation program?
I got deal with some annotation tool recently. I feel a bit confusing about some of their output result analysis
From the output result of that annotation program, it seems like shown that "gene = mRNA" region and "exon = CDS" region?
If you got experience in exploring annotation program, can I ask you opinions about it too?
Thanks again and a lot for your help first

As i said, a lot of them focus on CDS prediction and do not even consider UTRs (non coding parts of mRNAs exons), hence the "exon = CDS" -which is biologically wrong.
Also, regarding "gene=mRNA", prediction of alternative splicing variants is still a challenging area of bioinformatics research, so usually just one transcript is predicted by "gene".
Which software are you using? You can PM-me if you want (genome annotation is not really the main focus of this forum).